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Application of Bioinformatics to Asthma

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Book cover Genomic Approach to Asthma

Part of the book series: Translational Bioinformatics ((TRBIO,volume 12))

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Abstract

In this chapter, online database will be introduced step by step to acquire information regarding to Asthma. Phenotype and genotype are described in OMIM in detail, and a table of genes have something to do with Asthma could be downloaded. Overview of biological process of the genes can be analyzed by GO, and pathways got involved can be retrieved from KEGG. For a specific reported gene, comprehensive information is classified into different database in NCBI, and collection of function information is reviewed in Uniprot. For a novel gene candidate with only sequence, some advices for function prediction are suggested.

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Reference

  1. Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. OMIM.org: Online Mendelian Inheritance in Man (OMIM(R)), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 2015;43:D789–98. [PubMed: 25428349]

    Article  CAS  PubMed  Google Scholar 

  2. O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733–45. [PubMed: 26553804]

    Article  CAS  PubMed  Google Scholar 

  3. The UniProt C. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45:D158–69. [PubMed: 27899622]

    Article  CAS  Google Scholar 

  4. Gene Ontology C. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015;43:D1049–56. [PubMed: 25428369]

    Article  CAS  Google Scholar 

  5. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353–61. [PubMed: 27899662]

    Article  CAS  PubMed  Google Scholar 

  6. Brown GR, Hem V, Katz KS, Ovetsky M, Wallin C, Ermolaeva O, Tolstoy I, Tatusova T, Pruitt KD, Maglott DR, et al. Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 2015;43:D36–42. [PubMed: 25355515]

    Article  CAS  PubMed  Google Scholar 

  7. Lenzi L, Frabetti F, Facchin F, Casadei R, Vitale L, Canaider S, Carinci P, Zannotti M, Strippoli P. UniGene Tabulator: a full parser for the UniGene format. Bioinformatics. 2006;22:2570–1. [PubMed: 16895929]

    Article  CAS  PubMed  Google Scholar 

  8. Wolfsberg TG. Using the NCBI Map Viewer to browse genomic sequence data. 2011; Chapter 18:Unit18 5. [PubMed: 21480181].

  9. Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): the single global macromolecular structure archive. Methods Mol Biol. 2017;1607:627–41. [PubMed: 28573592]

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–11. [PubMed: 11125122]

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, et al. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013;41:D936–41. [PubMed: 23193291]

    Article  CAS  PubMed  Google Scholar 

  12. Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016;44:D862–8. [PubMed: 26582918]

    Article  CAS  PubMed  Google Scholar 

  13. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. [PubMed: 20003500]

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Bhagwat M, Aravind L. PSI-BLAST tutorial. BMC Bioinformatics. 2007;395:177–86. [PubMed: 17993673]

    CAS  Google Scholar 

  15. Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 2012;40:W597–603. [PubMed: 22661580]

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztanyi Z, El-Gebali S, Fraser M, et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017;45:D190–9. [PubMed: 27899635]

    Article  CAS  PubMed  Google Scholar 

  17. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10:845–58. [PubMed: 25950237]

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. School of Life Sciences and Technology, Tongji University, Shanghai, China

    Aiping Lu (Lyu), Dan Li, Yan Liu & Haiyun Wang

Authors
  1. Aiping Lu (Lyu)
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  2. Dan Li
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  3. Yan Liu
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  4. Haiyun Wang
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Corresponding author

Correspondence to Aiping Lu (Lyu) .

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Editors and Affiliations

  1. Zhongshan Hospital Institute of Clinical Science, Shanghai Medical School Fudan University, Shanghai, China

    Xiangdong Wang

  2. Shanghai Respiratory Research Institute, Respiratory Division of Zhongshan Hospital, Fudan University, Shanghai, China

    Zhihong Chen

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Lu (Lyu), A., Li, D., Liu, Y., Wang, H. (2018). Application of Bioinformatics to Asthma. In: Wang, X., Chen, Z. (eds) Genomic Approach to Asthma. Translational Bioinformatics, vol 12. Springer, Singapore. https://doi.org/10.1007/978-981-10-8764-6_16

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